Cytogenetics is the field of study of chromosomes during the metaphase stage of the cell life cycle. It is at this stage where chromosomes are at their highest point of condensation and are most convenient to study in both the normal and disease state. Currently the most frequently used technique in the cytogenetics field (worldwide) is either short term (<10 days) or long term (up to 45 days) culture of the specimen submitted for testing. Specimens comprise a number of varying types such as peripheral blood, bone marrow, amniotic fluid, solid tissue, products of conception, pleural effusion and the like. After successful culture, through various processes, metaphase chromosomes are generally obtained and read, to determine whether the individual tested has a genetic abnormality. This process is quite complex and requires the use of numerous chemicals and reagents as well as a significant amount of time and expertise.
Chromosomal studies are frequently requested for various diagnostic purposes including the following: 1) prenatal diagnosis; 2) Peripheral blood chromosome test (to test for patients with abnormal phenotypic features, mental retardation, couples with infertility issues as well as multiple miscarriage issues to determine whether the cause is genetic; 3) Leukemia/Lymphoma diagnosis (vital to both accurate diagnosis as well as management of drug protocols); and 4) solid tumor diagnosis and treatment management (for cancers including bladder, prostate, kidney, breast, lung and the like.
For nearly fifteen years, a technique called Fluorescent In Situ Hybridization (FISH) has been used to obtain the chromosome/karyotype information. This technique, however, is limited. Utilizing the FISH technique, complete karyotype information cannot be obtained. A significant amount of the FISH testing has been used on Interphase stage nuclei, where chromosomes are not visible by the routine cytogenetic techniques, without further culture. Recently, a more complete chromosomal analysis, or karyotype information, was possible using the multiplex FISH (M-FISH) technique. The problem with this technique was that one culture was still required to obtain chromosomes for testing. Only then could M-FISH clarify suspected abnormalities as well as detect new or unsuspected changes.
Even more recently, several multicolor banding techniques, such as multicolor banding (MCG), multicolor chromosome bar code technique, cross-species color banding technique (rx-FISH), spectral color banding technique (SCAN) were developed. Of all of these techniques, only MCG has been applied to Interphase chromosomes.
Most FISH-based techniques use disease-specific probes. When disease-specific probes are generated, the probe sets are limited to the existing knowledge of specific alterations such as translocations, deletions, inversions, amplifications or other known chromosomal anomalies. Without previous knowledge of a suspected genetic abnormality, Cytogeneticists were unable to make a diagnosis for an unknown or unsuspected genetic disorder. Utilizing whole chromosome paints, allows previously undetected translocations to be recognized. This, however, is a very cumbersome process and required the use of twenty-four (24) separate chromosome painting probe set. Furthermore, the process yields information only on a single type of genetic abnormality, namely, a translocation between two different chromosomes. Often in disease processes, genetic alterations comprise numerous manifestations including translocations, deletions or inversions. These other changes, especially, intrachromosomal changes cannot all be detected by current chromosome painting probe sets. Instead, they require yet another set or multiple sets of disease specific probes thereby becoming cost-prohibitive for the routine clinical cytogenetics laboratory.
Numerous additional draw backs exist with the above mentioned techniques, for studying the metaphase chromosomes, these include: very complex color banding patterns obtained to recognize individual human chromosomes; techniques that require the use of very expensive equipment such as filters, dichroic mirrors, CCD cameras, sophisticated computer software, inferometers and other specialized apparatus to interpret banding patterns; techniques that do not provide complete karyotype information, i.e., the detection of certain type of abnormalities, such as, Robertsonian translocations; each of the techniques are fluorochrome-based, wherein the fluorescence quenches or fades and the resulting banding pattern is not permanent; resulting banding patterns that are assigned psuedo-colors through the use of by computer software and cannot be interpreted by simple human observation; techniques, that while useful in a research setting, are not practical for routine use in clinical cytogenetics laboratories; and marker chromosomes that are structurally altered and generally cannot be traced, this is especially critical as marker chromosomes have both diagnostic as well as prognostic implications in numerous clinical situations.
One genetic abnormality is of particular importance in genetic diagnosis, this abnormality is referred to as a Robertsonian translocation. Robertsonian translocations are translocations between acrocentric chromosomes that join by their centromeres, resulting in one less centromere in the karyotype. Robertsonian transolocations are clinically significant particularly in prenatal diagnosis. A pathological condition called Uniparental Disomy (UPD) exists for chromosomes 13, 14, and 15. UPD in the fetus, detected in the prenatal diagnosis, contributes to severe clinical manifestations and significantly adds to infant morbidity rates.
The documents and publications cited in this disclosure are incorporated herein by reference in their entirety, to the extent they are not inconsistent with the explicit teachings set forth.